Featured Research

from universities, journals, and other organizations

Genomic imprinting of natural selection revealed

Date:
February 16, 2012
Source:
Universitat Auṭnoma de Barcelona
Summary:
Discovering the relation between genetic variation and observable characteristics of individuals belonging to a species, such as a person's height or the manifestation of a hereditary disease is one of today's challenges in biology. Until now only a small part of the variation of these traits - which biologists name phenotypes - were attributed to genetic variations.

Discovering the relation between genetic variation and observable characteristics of individuals belonging to a species, such as a person's height or the manifestation of a hereditary disease is one of today's challenges in biology. Until now only a small part of the variation of these traits -- which biologists name phenotypes -- were attributed to genetic variations.

To be able to analyse the relation between genes and phenotype, an international project was carried out. One of the main researchers was UAB professor Antonio Barbadilla and his research group ??Bioinformatics for Genetic Diversity, in collaboration with the Comparative Genomics and Bioinformatics group led by UB professor Julio Rozas. The project has achieved to obtain the complete sequence of the gene of 168 lines preceding from the same population of Drosophila melanogaster (the common fruit fly, a model species used in the studies of genetics). The lines can be consulted by any scientist interested in studying the genetic base of a given phenotype. This is a true in vivo library, maintained under laboratory conditions, which facilitates detecting genetic effects on the phenotype and permits discovering the genetic makeup of hereditary diseases.

The analysis of enormous amounts of data contained in the 168 complete genomes, a colossal task which required much efforts on behalf of specialists in bioinformatics and population genetics, is beginning to show results. The first ones can be read this week in Nature, which have been the detection of the mark left by natural selection all along the genome. A molecular signature natural selection has left on the genetic variation patterns seen in each region of the genome. All new mutation which contributes to adapting to the environment of an individual spreads rapidly to the rest of the species -- a process known as adaptive selection. In contrast, there are regions of the genome in which all types of mutations end up being harmful and are finally eliminated from the population, in a process known as negative selection. Both selection processes leave characteristic molecular signatures on the genome. Through the comparison of genomes of a large number of individuals of the same species and of other similar species, scientists have been able to trace the first high resolution map of the natural selection of a genome in both regions that code proteins and those that do not.

Researchers observed that the mark left by natural selection is present along the genome, although the importance of different types of selection continues to depend on the type of functional areas and on the genome regions considered. For example, scientists observed that selection is more intense and effective in the X chromosome than in the rest of chromosomes, which represents a more rapid evolution of this sex chromosome. Another relevant observation is that the genetic recombination rate (variable along the genome) plays a fundamental role in improving the ability of adaptive selection in different regions of the genome. The probability of a genomic region responding effectively to natural selection depends on its recombinational context. In a region with little or no recombination, selection will not be able to prevent the functional degradation of the region.

For UAB professor Antonio Barbadilla, one of the main researchers in the project, "having 168 genomes of a single natural population is a unique opportunity to carry out the most complete genome study of a species ever done." "For all population geneticist it is a dream come true to be able to use a set of data as large as the one in this project to test many hypotheses which have been disputed in the past decades," Barbadilla adds.

To calculate, store, manage and visualise all variation data in the genomes, UAB researchers in collaboration with UB researchers designed and used the recently created navigator for population genome data: the Population Drosophila Genome Browser (PopDrowser). The navigator graphically represents all information extracted from genome sequencing including DNA sequencing, genomic annotations, estimations of nucleotide diversity; and calculates several statistical tests to determine the effect of natural selection at nucleotide level. The PopDrowser navigator is described in an article published on line in the journal Bioinformatics and can be consulted at http://popdrowser.uab.cat.

This research has been developed by UAB Group in Bioinformatics for Genetic Diversity (David Castellano, Miquel Ràmia, Ṣnia Casillas and Maite Barrón, leaded by Antonio Barbadilla); and the UB Group in Comparative Genomics and Bioinformatics leaded by Julio Rozas.


Story Source:

The above story is based on materials provided by Universitat Auṭnoma de Barcelona. Note: Materials may be edited for content and length.


Journal Reference:

  1. Trudy F. C. Mackay, Stephen Richards, Eric A. Stone, Antonio Barbadilla, Julien F. Ayroles, Dianhui Zhu, Ṣnia Casillas, Yi Han, Michael M. Magwire, Julie M. Cridland, Mark F. Richardson, Robert R. H. Anholt, Maite Barrón, Crystal Bess, Kerstin Petra Blankenburg, Mary Anna Carbone, David Castellano, Lesley Chaboub, Laura Duncan, Zeke Harris, Mehwish Javaid, Joy Christina Jayaseelan, Shalini N. Jhangiani, Katherine W. Jordan, Fremiet Lara, Faye Lawrence, Sandra L. Lee, Pablo Librado, Raquel S. Linheiro, Richard F. Lyman, Aaron J. Mackey, Mala Munidasa, Donna Marie Muzny, Lynne Nazareth, Irene Newsham, Lora Perales, Ling-Ling Pu, Carson Qu, Miquel Ràmia, Jeffrey G. Reid, Stephanie M. Rollmann, Julio Rozas, Nehad Saada, Lavanya Turlapati, Kim C. Worley, Yuan-Qing Wu, Akihiko Yamamoto, Yiming Zhu, Casey M. Bergman, Kevin R. Thornton, David Mittelman, Richard A. Gibbs. The Drosophila melanogaster Genetic Reference Panel. Nature, 2012; 482 (7384): 173 DOI: 10.1038/nature10811

Cite This Page:

Universitat Auṭnoma de Barcelona. "Genomic imprinting of natural selection revealed." ScienceDaily. ScienceDaily, 16 February 2012. <www.sciencedaily.com/releases/2012/02/120216111532.htm>.
Universitat Auṭnoma de Barcelona. (2012, February 16). Genomic imprinting of natural selection revealed. ScienceDaily. Retrieved July 25, 2014 from www.sciencedaily.com/releases/2012/02/120216111532.htm
Universitat Auṭnoma de Barcelona. "Genomic imprinting of natural selection revealed." ScienceDaily. www.sciencedaily.com/releases/2012/02/120216111532.htm (accessed July 25, 2014).

Share This




More Plants & Animals News

Friday, July 25, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

How to Make Single Serving Smoothies: Howdini Hacks

How to Make Single Serving Smoothies: Howdini Hacks

Howdini (July 24, 2014) — Smoothies are a great way to get in lots of healthy ingredients, plus they taste great! Howdini has a trick for making the perfect single-size smoothie that will save you time on cleanup too! All you need is a blender and a mason jar. Video provided by Howdini
Powered by NewsLook.com
Boy Attacked by Shark in Florida

Boy Attacked by Shark in Florida

Reuters - US Online Video (July 24, 2014) — An 8-year-old boy is bitten in the leg by a shark while vacationing at a Florida beach. Linda So reports. Video provided by Reuters
Powered by NewsLook.com
Goma Cheese Brings Whiff of New Hope to DRC

Goma Cheese Brings Whiff of New Hope to DRC

Reuters - Business Video Online (July 24, 2014) — The eastern region of the Democratic Republic of Congo, mainly known for conflict and instability, is an unlikely place for the production of fine cheese. But a farm in the village of Masisi, in North Kivu is slowly transforming perceptions of the area. Known simply as Goma cheese, the Congolese version of Dutch gouda has gained popularity through out the region. Ciara Sutton reports. Video provided by Reuters
Powered by NewsLook.com
Tyrannosaur Pack-Hunting Theory Aided By New Footprints

Tyrannosaur Pack-Hunting Theory Aided By New Footprints

Newsy (July 24, 2014) — A new study claims a set of prehistoric T-Rex footprints supports the theory that the giant predators hunted in packs instead of alone. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
 
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:  

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

    Health News

      Environment News

        Technology News



          Save/Print:
          Share:  

          Free Subscriptions


          Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

          Get Social & Mobile


          Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

          Have Feedback?


          Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
          Mobile iPhone Android Web
          Follow Facebook Twitter Google+
          Subscribe RSS Feeds Email Newsletters
          Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins